Made the sub-parameters for intersection-rate, similarity-threshold,...

Made the sub-parameters for intersection-rate, similarity-threshold, mcl-inflation and contrast in Group.java mutually dependent. Added a table including their values for each relaxation settings in the read the docs manual.

docs/source/tables/relaxation.csv

+Relaxation;1;2;3;4;5;6;7;8
+Intersection rate;0.08;0.07;0.06;0.05;0.04;0.03;0.02;0.01
+Similarity threshold;95;85;75;65;55;45;35;25
+Mcl inflation;10.8;9.6;8.4;7.2;6.0;4.8;3.6;2.4
+Contrast;8;7;6;5;4;3;2;1
\ No newline at end of file

docs/source/user_guide/construct.rst

@@ -203,20 +203,35 @@ of the sequence.
 When you want to run **group** another time but with different
 parameters, the currently active grouping must first either be moved or
 removed. This can be achieved with the
-:ref:`move- or remove_homology_groups <construct:move or remove grouping>`
+:ref:`move or remove grouping <construct:move or remove grouping>`
 functions.
 
-| **Method**
-| Here, we explain a simplified version of the original algorithm,
-  please take a look at our publication for an extensive explanation.
-  First, potential similar sequences are identified by counting shared
-  *k*-mer (protein) sequences. Similarity between the selected protein
-  sequences is calculated through (local) Smith-Waterman alignments.
-  When the (normalized) similarity score of two sequences is above a
-  given threshold (controlled by ``--relaxation``), the proteins are
-  connected with each other in the similarity graph. Every similarity
-  component is then passed to the MCL (Markov clustering) algorithm to
-  be possibly broken into several homology groups.
+Method
+""""""
+Here, we explain a simplified version of the original algorithm,
+please take a look at our publication for an extensive explanation.
+First, potential similar sequences are identified by counting shared
+*k*-mer (protein) sequences. Similarity between the selected protein
+sequences is calculated through (local) Smith-Waterman alignments.
+When the (normalized) similarity score of two sequences is above a
+given threshold (controlled by ``--relaxation``), the proteins are
+connected with each other in the similarity graph. Every similarity
+component is then passed to the MCL (Markov clustering) algorithm to
+be possibly broken into several homology groups.
+
+Relaxation
+""""""""""
+The ``relaxation`` parameter is a combination of four sub-parameters:
+``intersection rate``, ``similarity threshold``, ``mcl inflation``
+and ``contrast``. The values for these parameter for each relaxation
+setting can be seen in the table below. We recommend using the
+``--relaxation`` option if there is any uncertainty about its
+sub-parameters.
+
+.. csv-table::
+   :file: tables/relaxation.csv
+   :header-rows: 1
+   :delim: ;
 
 Required software
 """""""""""""""""
@@ -253,18 +268,18 @@ Options
      - Only cluster protein sequences of the longest transcript per gene.
    * - ``--relaxation``
      - The relaxation in homology calls. Should be in range [1-8], from
-       strict to relaxed (default 1). This argument automatically sets
+       strict to relaxed. This argument automatically sets
        the four remaining arguments stated below.
    * - ``--intersection-rate``
      - The fraction of *k*-mers that needs to be shared by two intersecting
-       proteins. Should be in range [0.001,0.1] (default: 0.08).
+       proteins. Should be in range [0.001,0.1].
    * - ``--similarity-threshold``
      - The minimum normalized similarity score of two proteins. Should be in
-       range [1..99] (default: 95).
+       range [1..99].
    * - ``--mcl-inflation``
-     - The MCL inflation. Should be in range [1,19] (default: 10.8).
+     - The MCL inflation. Should be in range [1,19].
    * - ``--contrast``
-     - The contrast factor. Should be in range [0,10] (default: 8).
+     - The contrast factor. Should be in range [0,10].
 
 Example commands
 """"""""""""""""

src/main/java/nl/wur/bif/pantools/cli/Group.java

@@ -43,19 +43,19 @@ public class Group implements Callable<Integer> {
 
     @DecimalMin(value = "0.001", message = "{range.ir}")
     @DecimalMax(value = "0.1", message = "{range.ir")
-    static double intersectionRate = 0.05;
+    static double intersectionRate;
 
     @Min(value = 1, message = "{min.st}")
     @Max(value = 99, message = "{max.st}")
-    static int similarityThreshold = 65;
+    static int similarityThreshold;
 
     @Min(value = 1, message = "{min.mcl-i}")
     @Max(value = 99, message = "{max.mcl-i}")
-    static double mclInflation = 7.2;
+    static double mclInflation;
 
     @DecimalMin(value = "0", message = "{min.contrast}")
     @DecimalMax(value = "10", message = "{max.contrast}")
-    static double contrast = 5;
+    static double contrast;
 
     @ArgGroup(multiplicity = "1") RelaxationSettings relaxationSettings;
     private static class RelaxationSettings {
@@ -75,16 +75,16 @@ public class Group implements Callable<Integer> {
     }
 
     private static class RelaxationParameters {
-        @Option(names = "--intersection-rate")
+        @Option(names = "--intersection-rate", required = true)
         void setIntersectionRate(double value) {intersectionRate = value;}
 
-        @Option(names = "--similarity-threshold")
+        @Option(names = "--similarity-threshold", required = true)
         void setSimilarityThreshold(int value) {similarityThreshold = value;}
 
-        @Option(names = "--mcl-inflation")
+        @Option(names = "--mcl-inflation", required = true)
         void setMclInflation(double value) {mclInflation = value;}
 
-        @Option(names = "--contrast")
+        @Option(names = "--contrast", required = false)
         void setContrast(double value) {contrast = value;}
     }
 

src/main/resources/Defaults.properties

@@ -18,11 +18,6 @@ pantools.core_phylogeny.clustering-mode = ML
 pantools.create_tree_template.color = 2
 # GoEnrichment
 pantools.go_enrichment.fdr = 5
-# Group
-pantools.group.intersection-rate = 0.05
-pantools.group.similarity-threshold = 65
-pantools.group.mcl-inflation = 7.2
-pantools.group.contrast = 5
 # LocateGenes
 pantools.locate_genes.core-threshold = 0
 pantools.locate_genes.gap-open = 0

src/main/resources/MessageBundle.properties

@@ -169,8 +169,6 @@ proteomes-file = A text file containing paths to FASTA files of proteins to be a
 include = Only include a selection of genomes.
 regions-file = A text file containing genome locations with on each line: a genome number, sequence number, begin and \
   end position, separated by a space.
-similarity-threshold = The minimum normalized similarity score of two proteins. Should be in range [1..99] (default: \
-  ${DEFAULT-VALUE}).
 threads = Number of parallel working threads, default is the number of cores or 8, whichever is lower.
 unique-threshold = Threshold (%%) for unique/cloud genes. Default is a single genome, not a percentage.
 
@@ -244,10 +242,12 @@ pantools.gene_classification.phenotype = A phenotype name, used to find genes sp
 # GoEnrichment
 pantools.go_enrichment.fdr = The false discovery rate (%%) (default: ${DEFAULT-VALUE}%%).
 # Group
-pantools.group.contrast = The contrast factor. Should be in range [0,10] (default: ${DEFAULT-VALUE}).
+pantools.group.contrast = The contrast factor. Should be in range [0,10].
 pantools.group.intersection-rate = The fraction of k-mers that needs to be shared by two intersecting proteins. Should \
-  be in range [0.001,0.1] (default: ${DEFAULT-VALUE}).
-pantools.group.mcl-inflation = The MCL inflation. Should be in range [1,19] (default: ${DEFAULT-VALUE}).
+  be in range [0.001,0.1].
+pantools.group.mcl-inflation = The MCL inflation. Should be in range [1,19].
+pantools.group.similarity-threshold = The minimum normalized similarity score of two proteins. \
+  Should be in range [1..99].
 pantools.group.relaxation = The relaxation in homology calls. Should be in range [1..8], from strict to relaxed. \
   Use optimal_grouping to determine the best relaxation setting.
 # GroupInfo